Great thought Libra and one that has many answers.
You could say that Will's destiny was determind when Bootstrap was sent to the depths, or maybe it was when Will forged, what started off as Norrington's sword. It was that sword that killed Will...

... there was certainly a touch of destiny about that.
I think that it was Jack who actually determind Will's fate. He wanted to be 'the immortal Captain Jack Sparrow', he gave that up in the first film, so in AWE along came his chance again, but again he gave that up for Will. Jack took Will's hand and helped him stab the heart, it wasn't until that moment that his destiny was decided...

...after all, given the opportunity, Jack would have done that very deed himself.
You can also go way back to when Will was a child. Bootstrap gave him the piece of Aztec Gold, so that the Pirates would remain cursed forever. Maybe his fate was determind then because that gold found its way back to Will, bringing him together with Elizabeth, bringing the Pirates to Port Royal, bringing Jack Sparrow into his life..and so on and so forth.
Definitely lots to think about.